Variant report

Variant	rs16959197
Chromosome Location	chr16:12411508-12411509
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12384757..12387424-chr16:12410690..12412315,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1032887	0.87[ASN][1000 genomes]
rs10500380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs13331380	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13332083	0.83[ASN][1000 genomes]
rs13332306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16959078	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16959097	0.87[ASN][1000 genomes]
rs16959100	0.87[ASN][1000 genomes]
rs16959126	0.87[ASN][1000 genomes]
rs16959130	0.87[ASN][1000 genomes]
rs16959253	0.83[ASN][1000 genomes]
rs16959350	1.00[CEU][hapmap];0.85[MEX][hapmap]
rs28372578	0.83[ASN][1000 genomes]
rs28472378	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28496413	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs41325045	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs56836971	0.83[ASN][1000 genomes]
rs57011047	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs60011426	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs60280624	0.87[ASN][1000 genomes]
rs61159108	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73508005	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs746311	0.83[ASN][1000 genomes]
rs746312	0.83[ASN][1000 genomes]
rs8058627	0.87[ASN][1000 genomes]
rs870641	0.87[ASN][1000 genomes]
rs905948	0.87[ASN][1000 genomes]
rs9922894	0.83[ASN][1000 genomes]
rs9926796	1.00[CEU][hapmap];0.85[MEX][hapmap]
rs9927344	0.87[ASN][1000 genomes]
rs9929445	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9932158	1.00[CEU][hapmap]
rs9933058	0.83[ASN][1000 genomes]
rs9940308	1.00[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv457411	chr16:12363304-12520199	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv571462	chr16:12363304-12520199	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1045385	chr16:12376389-12517006	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv542748	chr16:12376389-12517006	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv905349	chr16:12408750-12445863	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12359800-12418000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr16:12371400-12456800	Weak transcription	Aorta	Aorta
3	chr16:12373400-12414200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr16:12374200-12417200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr16:12395400-12413800	Weak transcription	Left Ventricle	heart
6	chr16:12395600-12417200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr16:12396000-12414800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr16:12396200-12414000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr16:12396800-12416400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr16:12404000-12414800	Weak transcription	Thymus	Thymus
11	chr16:12404200-12427400	Weak transcription	Primary T cells from cord blood	blood
12	chr16:12404600-12413400	Weak transcription	Fetal Heart	heart
13	chr16:12405200-12411800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr16:12405600-12412800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr16:12405600-12413200	Weak transcription	Right Ventricle	heart
16	chr16:12405600-12426400	Weak transcription	Lung	lung
17	chr16:12405600-12442400	Weak transcription	Spleen	Spleen
18	chr16:12405800-12413200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr16:12405800-12417800	Weak transcription	Adipose Nuclei	Adipose
20	chr16:12406200-12413200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr16:12407400-12412200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr16:12407800-12411600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr16:12407800-12412800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr16:12408000-12411800	Enhancers	NHEK	skin
25	chr16:12408200-12411800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr16:12408200-12411800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr16:12408200-12412400	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr16:12408400-12411800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr16:12408800-12417200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr16:12409000-12414000	Weak transcription	NHDF-Ad	bronchial
31	chr16:12409400-12413400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr16:12409400-12417400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr16:12409400-12417600	Weak transcription	Fetal Intestine Small	intestine
34	chr16:12409400-12417800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr16:12409600-12413200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr16:12409600-12413400	Weak transcription	Fetal Stomach	stomach
37	chr16:12409800-12413400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr16:12410000-12411600	Weak transcription	Ovary	ovary
39	chr16:12410000-12413400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr16:12410000-12413400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr16:12410000-12413800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr16:12410000-12414400	Weak transcription	Fetal Thymus	thymus
43	chr16:12410000-12456600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr16:12410200-12411600	Enhancers	Primary B cells from cord blood	blood
45	chr16:12410200-12413000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr16:12410200-12413400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr16:12410200-12424400	Weak transcription	Right Atrium	heart
48	chr16:12410200-12464800	Weak transcription	Gastric	stomach
49	chr16:12410400-12412000	Genic enhancers	Esophagus	oesophagus
50	chr16:12410600-12415000	Weak transcription	Pancreas	Pancrea

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